FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 76VYK

Calculation Name: 2ERF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ERF

Chain ID: A

ChEMBL ID:

UniProt ID: P07996

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 208
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2421690.979701
FMO2-HF: Nuclear repulsion 2342124.820523
FMO2-HF: Total energy -79566.159178
FMO2-MP2: Total energy -79800.884666


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:7:GLY)


Summations of interaction energy for fragment #1(A:7:GLY)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-7.361-2.9544.756-4.554-4.609-0.038
Interaction energy analysis for fragmet #1(A:7:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.008
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A9ASP-1-0.899-0.9473.797-2.834-1.818-0.011-0.577-0.4270.001
4A10ASN0-0.067-0.0355.9250.0720.0720.0000.0000.0000.000
5A11SER00.0280.0092.622-1.777-0.5181.207-1.260-1.206-0.007
6A12VAL00.0020.0004.4770.0350.190-0.001-0.012-0.1410.000
7A13PHE00.0140.0127.0690.1820.1820.0000.0000.0000.000
8A14ASP-1-0.790-0.88510.771-0.280-0.2800.0000.0000.0000.000
9A15ILE00.0390.00613.4190.0350.0350.0000.0000.0000.000
10A16PHE00.004-0.01516.3850.0310.0310.0000.0000.0000.000
11A17GLU-1-0.981-0.98414.996-0.426-0.4260.0000.0000.0000.000
12A18LEU0-0.013-0.00913.4790.0250.0250.0000.0000.0000.000
13A19THR0-0.054-0.01617.7830.0330.0330.0000.0000.0000.000
14A20GLY00.0320.01720.8040.0220.0220.0000.0000.0000.000
15A21ALA00.0070.00122.7030.0220.0220.0000.0000.0000.000
16A22ALA00.0070.00422.8840.0170.0170.0000.0000.0000.000
17A23ARG10.9170.95621.2230.2310.2310.0000.0000.0000.000
18A24LYS10.9891.00326.7360.1310.1310.0000.0000.0000.000
19A25GLY0-0.007-0.01628.9760.0000.0000.0000.0000.0000.000
20A26SER0-0.017-0.00831.0760.0060.0060.0000.0000.0000.000
21A27GLY00.0820.04830.113-0.007-0.0070.0000.0000.0000.000
22A28ARG10.8440.92727.0410.1290.1290.0000.0000.0000.000
23A29ARG10.9931.02430.2030.0680.0680.0000.0000.0000.000
24A30LEU0-0.025-0.00225.602-0.003-0.0030.0000.0000.0000.000
25A31VAL0-0.086-0.05427.3420.0120.0120.0000.0000.0000.000
26A32LYS10.9850.98326.5700.0630.0630.0000.0000.0000.000
27A33GLY00.0340.00423.7520.0030.0030.0000.0000.0000.000
28A34PRO0-0.044-0.01821.0880.0010.0010.0000.0000.0000.000
29A35ASP-1-0.722-0.81717.381-0.166-0.1660.0000.0000.0000.000
30A36PRO0-0.033-0.01520.639-0.007-0.0070.0000.0000.0000.000
31A37SER0-0.091-0.06418.547-0.007-0.0070.0000.0000.0000.000
32A38SER00.0250.01218.085-0.012-0.0120.0000.0000.0000.000
33A39PRO0-0.034-0.01320.0250.0220.0220.0000.0000.0000.000
34A40ALA00.0240.01821.519-0.011-0.0110.0000.0000.0000.000
35A41PHE0-0.005-0.01721.0380.0080.0080.0000.0000.0000.000
36A42ARG10.9370.96825.6540.0680.0680.0000.0000.0000.000
37A43ILE0-0.005-0.01125.317-0.003-0.0030.0000.0000.0000.000
38A44GLU-1-0.964-0.98829.345-0.071-0.0710.0000.0000.0000.000
39A45ASP-1-0.849-0.94231.838-0.071-0.0710.0000.0000.0000.000
40A46ALA00.012-0.00827.895-0.006-0.0060.0000.0000.0000.000
41A47ASN0-0.041-0.01228.752-0.010-0.0100.0000.0000.0000.000
42A48LEU0-0.022-0.01530.741-0.004-0.0040.0000.0000.0000.000
43A49ILE0-0.0320.00524.651-0.005-0.0050.0000.0000.0000.000
44A50PRO0-0.027-0.00224.7260.0060.0060.0000.0000.0000.000
45A51PRO0-0.011-0.01023.467-0.006-0.0060.0000.0000.0000.000
46A52VAL0-0.005-0.00616.847-0.009-0.0090.0000.0000.0000.000
47A53PRO0-0.0170.00019.1110.0200.0200.0000.0000.0000.000
48A54ASP-1-0.807-0.90519.165-0.194-0.1940.0000.0000.0000.000
49A55ASP-1-0.874-0.93918.367-0.317-0.3170.0000.0000.0000.000
50A56LYS10.9650.98214.9840.4520.4520.0000.0000.0000.000
51A57PHE0-0.005-0.00814.308-0.033-0.0330.0000.0000.0000.000
52A58GLN00.0220.00015.2580.0180.0180.0000.0000.0000.000
53A59ASP-1-0.870-0.92711.354-0.494-0.4940.0000.0000.0000.000
54A60LEU0-0.067-0.02010.545-0.026-0.0260.0000.0000.0000.000
55A61VAL0-0.058-0.02711.4170.0500.0500.0000.0000.0000.000
56A62ASP-1-0.781-0.89612.171-0.175-0.1750.0000.0000.0000.000
57A63ALA00.0180.0257.2560.0670.0670.0000.0000.0000.000
58A64VAL0-0.0180.0008.9210.1420.1420.0000.0000.0000.000
59A65ARG10.7470.86011.0890.2000.2000.0000.0000.0000.000
60A66THR0-0.099-0.0498.3080.0390.0390.0000.0000.0000.000
61A67GLU-1-0.865-0.9386.2790.7180.7180.0000.0000.0000.000
62A68LYS10.8780.9479.364-0.107-0.1070.0000.0000.0000.000
63A69GLY00.0410.01311.5870.0170.0170.0000.0000.0000.000
64A70PHE00.0240.0029.307-0.050-0.0500.0000.0000.0000.000
65A71LEU00.0170.0327.8000.0720.0720.0000.0000.0000.000
66A72LEU0-0.052-0.0239.881-0.140-0.1400.0000.0000.0000.000
67A73LEU00.0030.0119.6750.0610.0610.0000.0000.0000.000
68A74ALA00.021-0.00113.487-0.037-0.0370.0000.0000.0000.000
69A75SER00.0130.03816.9760.0240.0240.0000.0000.0000.000
70A76LEU0-0.030-0.02519.847-0.016-0.0160.0000.0000.0000.000
71A77ARG10.9330.98523.2240.0500.0500.0000.0000.0000.000
72A78GLN00.0280.03626.872-0.004-0.0040.0000.0000.0000.000
73A79MET0-0.026-0.01328.7660.0070.0070.0000.0000.0000.000
74A80LYS10.9860.99632.2320.0150.0150.0000.0000.0000.000
75A81LYS10.9670.98433.8850.0040.0040.0000.0000.0000.000
76A82THR0-0.039-0.02831.911-0.002-0.0020.0000.0000.0000.000
77A83ARG10.8810.93830.4650.0280.0280.0000.0000.0000.000
78A84GLY00.0060.00328.251-0.002-0.0020.0000.0000.0000.000
79A85THR0-0.008-0.01224.5390.0030.0030.0000.0000.0000.000
80A86LEU0-0.027-0.01820.225-0.007-0.0070.0000.0000.0000.000
81A87LEU00.0140.00516.920-0.019-0.0190.0000.0000.0000.000
82A88ALA00.0160.00321.4850.0170.0170.0000.0000.0000.000
83A89LEU0-0.045-0.00318.251-0.016-0.0160.0000.0000.0000.000
84A90GLU-1-0.876-0.94622.460-0.087-0.0870.0000.0000.0000.000
85A91ARG11.0151.00125.7730.0520.0520.0000.0000.0000.000
86A92LYS10.7830.87724.9120.1420.1420.0000.0000.0000.000
87A93ASP-1-0.852-0.87529.110-0.064-0.0640.0000.0000.0000.000
88A94HIS0-0.035-0.02531.3460.0050.0050.0000.0000.0000.000
89A95SER0-0.071-0.06132.2160.0050.0050.0000.0000.0000.000
90A96GLY00.0240.01030.8260.0060.0060.0000.0000.0000.000
91A97GLN0-0.028-0.01525.807-0.003-0.0030.0000.0000.0000.000
92A98VAL00.006-0.01122.3860.0080.0080.0000.0000.0000.000
93A99PHE00.0420.00717.8360.0050.0050.0000.0000.0000.000
94A100SER0-0.057-0.02422.365-0.011-0.0110.0000.0000.0000.000
95A101VAL00.0760.05918.5140.0120.0120.0000.0000.0000.000
96A102VAL0-0.016-0.01621.979-0.013-0.0130.0000.0000.0000.000
97A103SER00.0240.00824.3260.0120.0120.0000.0000.0000.000
98A104ASN00.032-0.00225.801-0.006-0.0060.0000.0000.0000.000
99A105GLY00.0480.00729.2220.0060.0060.0000.0000.0000.000
100A106LYS10.7800.88131.3800.0240.0240.0000.0000.0000.000
101A107ALA00.0130.01231.6400.0020.0020.0000.0000.0000.000
102A108GLY0-0.042-0.00330.6870.0040.0040.0000.0000.0000.000
103A109THR00.0350.00727.7340.0040.0040.0000.0000.0000.000
104A110LEU0-0.033-0.01720.073-0.010-0.0100.0000.0000.0000.000
105A111ASP-1-0.778-0.86524.6710.0010.0010.0000.0000.0000.000
106A112LEU0-0.008-0.00420.032-0.013-0.0130.0000.0000.0000.000
107A113SER0-0.0150.00123.3140.0110.0110.0000.0000.0000.000
108A114LEU00.0460.01920.265-0.012-0.0120.0000.0000.0000.000
109A115THR0-0.040-0.01824.3250.0080.0080.0000.0000.0000.000
110A116VAL00.0370.01424.216-0.007-0.0070.0000.0000.0000.000
111A117GLN0-0.047-0.03026.9190.0000.0000.0000.0000.0000.000
112A118GLY00.0040.00129.9060.0030.0030.0000.0000.0000.000
113A119LYS10.9430.97830.6200.0000.0000.0000.0000.0000.000
114A120GLN00.0200.01229.1720.0020.0020.0000.0000.0000.000
115A121HIS10.8520.93326.686-0.003-0.0030.0000.0000.0000.000
116A122VAL00.015-0.00326.825-0.005-0.0050.0000.0000.0000.000
117A123VAL00.0170.02624.4010.0030.0030.0000.0000.0000.000
118A124SER0-0.010-0.01525.967-0.007-0.0070.0000.0000.0000.000
119A125VAL0-0.017-0.00621.7770.0070.0070.0000.0000.0000.000
120A126GLU-1-0.875-0.96225.2020.0140.0140.0000.0000.0000.000
121A127GLU-1-0.904-0.94627.0680.0510.0510.0000.0000.0000.000
122A128ALA0-0.0010.00724.5950.0040.0040.0000.0000.0000.000
123A129LEU0-0.027-0.02526.473-0.009-0.0090.0000.0000.0000.000
124A130LEU00.0210.01022.9300.0000.0000.0000.0000.0000.000
125A131ALA0-0.0350.00226.639-0.006-0.0060.0000.0000.0000.000
126A132THR00.027-0.00828.8180.0030.0030.0000.0000.0000.000
127A133GLY0-0.065-0.03130.7700.0020.0020.0000.0000.0000.000
128A134GLN0-0.061-0.04429.562-0.005-0.0050.0000.0000.0000.000
129A135TRP0-0.035-0.02722.798-0.001-0.0010.0000.0000.0000.000
130A136LYS10.9631.00923.4020.0010.0010.0000.0000.0000.000
131A137SER00.0210.01317.454-0.027-0.0270.0000.0000.0000.000
132A138ILE0-0.046-0.02017.5160.0210.0210.0000.0000.0000.000
133A139THR00.0150.00312.308-0.030-0.0300.0000.0000.0000.000
134A140LEU0-0.023-0.00914.3220.0300.0300.0000.0000.0000.000
135A141PHE00.0140.0029.805-0.028-0.0280.0000.0000.0000.000
136A142VAL00.0210.00213.0800.0020.0020.0000.0000.0000.000
137A143GLN00.0050.00911.2120.0010.0010.0000.0000.0000.000
138A144GLU-1-0.862-0.93714.7780.1440.1440.0000.0000.0000.000
139A145ASP-1-0.891-0.94617.3470.0870.0870.0000.0000.0000.000
140A146ARG10.9721.00616.129-0.240-0.2400.0000.0000.0000.000
141A147ALA0-0.002-0.00317.6020.0050.0050.0000.0000.0000.000
142A148GLN0-0.004-0.00116.4270.0250.0250.0000.0000.0000.000
143A149LEU0-0.021-0.01016.720-0.009-0.0090.0000.0000.0000.000
144A150TYR00.0360.01215.3630.0210.0210.0000.0000.0000.000
145A151ILE0-0.045-0.03618.508-0.026-0.0260.0000.0000.0000.000
146A152ASP-1-0.845-0.93020.3970.0150.0150.0000.0000.0000.000
147A153CYS0-0.166-0.07614.3660.0000.0000.0000.0000.0000.000
148A154GLU-1-0.902-0.94920.8390.0620.0620.0000.0000.0000.000
149A155LYS10.8410.94922.341-0.041-0.0410.0000.0000.0000.000
150A156MET00.005-0.00619.3710.0110.0110.0000.0000.0000.000
151A157GLU-1-0.870-0.91421.5960.0640.0640.0000.0000.0000.000
152A158ASN0-0.020-0.03920.7460.0090.0090.0000.0000.0000.000
153A159ALA0-0.009-0.00121.999-0.010-0.0100.0000.0000.0000.000
154A160GLU-1-0.930-0.95422.2250.0950.0950.0000.0000.0000.000
155A161LEU0-0.079-0.04919.582-0.015-0.0150.0000.0000.0000.000
156A162ASP-1-0.856-0.93423.9290.0340.0340.0000.0000.0000.000
157A163VAL0-0.068-0.03522.991-0.002-0.0020.0000.0000.0000.000
158A164PRO00.0290.02319.489-0.001-0.0010.0000.0000.0000.000
159A165ILE00.0420.02915.190-0.023-0.0230.0000.0000.0000.000
160A166GLN0-0.003-0.03015.409-0.028-0.0280.0000.0000.0000.000
161A167SER0-0.089-0.04817.085-0.016-0.0160.0000.0000.0000.000
162A168VAL0-0.035-0.01419.776-0.008-0.0080.0000.0000.0000.000
163A169PHE0-0.0150.00115.528-0.018-0.0180.0000.0000.0000.000
164A170THR00.0310.00417.122-0.005-0.0050.0000.0000.0000.000
165A171ARG10.9810.95118.1620.0650.0650.0000.0000.0000.000
166A172ASP-1-0.834-0.89819.222-0.137-0.1370.0000.0000.0000.000
167A173LEU0-0.0420.00218.8690.0040.0040.0000.0000.0000.000
168A174ALA00.0320.01319.1050.0050.0050.0000.0000.0000.000
169A175SER0-0.035-0.02121.1210.0060.0060.0000.0000.0000.000
170A176ILE0-0.035-0.01924.2710.0110.0110.0000.0000.0000.000
171A177ALA0-0.033-0.01822.8730.0110.0110.0000.0000.0000.000
172A178ARG10.9910.99322.2200.1150.1150.0000.0000.0000.000
173A179LEU00.0110.02916.7140.0170.0170.0000.0000.0000.000
174A180ARG10.7940.88820.7840.1180.1180.0000.0000.0000.000
175A181ILE00.0650.02419.1330.0040.0040.0000.0000.0000.000
176A182ALA0-0.044-0.02722.5310.0090.0090.0000.0000.0000.000
177A183LYS10.9000.95825.0710.1000.1000.0000.0000.0000.000
178A184GLY00.011-0.00826.366-0.006-0.0060.0000.0000.0000.000
179A185GLY00.0180.02028.5330.0040.0040.0000.0000.0000.000
180A186VAL0-0.0070.00631.289-0.003-0.0030.0000.0000.0000.000
181A187ASN0-0.048-0.04234.8810.0010.0010.0000.0000.0000.000
182A188ASP-1-0.776-0.85430.259-0.035-0.0350.0000.0000.0000.000
183A189ASN00.0320.01429.219-0.006-0.0060.0000.0000.0000.000
184A190PHE0-0.016-0.00925.6290.0060.0060.0000.0000.0000.000
185A191GLN00.0170.01328.3410.0000.0000.0000.0000.0000.000
186A192GLY00.000-0.01429.1620.0070.0070.0000.0000.0000.000
187A193VAL0-0.088-0.04025.359-0.005-0.0050.0000.0000.0000.000
188A194LEU00.0400.02721.5350.0070.0070.0000.0000.0000.000
189A195GLN00.007-0.02419.3520.0110.0110.0000.0000.0000.000
190A196ASN0-0.010-0.00215.308-0.007-0.0070.0000.0000.0000.000
191A197VAL00.0140.01515.3090.0080.0080.0000.0000.0000.000
192A198ARG10.8660.91410.6600.3710.3710.0000.0000.0000.000
193A199PHE00.0230.0169.9060.0920.0920.0000.0000.0000.000
194A200VAL0-0.032-0.0204.532-0.199-0.176-0.001-0.003-0.0200.000
195A201PHE0-0.014-0.0043.9620.1990.3670.000-0.074-0.0940.000
196A202GLY00.012-0.0042.297-6.262-4.5763.513-2.953-2.246-0.030
197A203THR0-0.021-0.0133.4251.6531.7560.0500.330-0.484-0.002
198A204THR00.0630.0364.907-0.493-0.496-0.001-0.0050.0090.000
199A205PRO00.0360.0028.695-0.066-0.0660.0000.0000.0000.000
200A206GLU-1-0.975-0.97711.4570.4980.4980.0000.0000.0000.000
201A207ASP-1-0.841-0.9268.3321.2351.2350.0000.0000.0000.000
202A208ILE0-0.021-0.0027.733-0.127-0.1270.0000.0000.0000.000
203A209LEU00.012-0.00410.741-0.070-0.0700.0000.0000.0000.000
204A210ARG10.9240.96113.734-0.363-0.3630.0000.0000.0000.000
205A211ASN0-0.030-0.0069.582-0.012-0.0120.0000.0000.0000.000
206A212LYS10.8620.92313.733-0.194-0.1940.0000.0000.0000.000
207A213GLY0-0.0060.00413.434-0.038-0.0380.0000.0000.0000.000
208A215SER00.0360.00516.525-0.001-0.0010.0000.0000.0000.000